[Bioc-devel] eSet class and two color arrays

[Seth Falcon]

Wolfgang Huber <huber at ebi.ac.uk> writes:

> sorry, I used inexact language in the previous mail: of course there is
> always exactly one assayData slot, but that may contain one or several
> matrices of equal dimensions.

:-)

>> one of the basic features of the eSet class is that
>> - it has exactly one phenoData slot, and >=1 assayData slots
>> - the rows of the dataframe in phenoData correspond 1:1 to the columns
>>   of each the assayData matrices.
>> 
>> I was wondering whether there is interest in a class that has
>> - one or several phenoData slots, and the same number of assayData slots
>> - there is a 1:1 correspondence between these
>> - the rows of each phenoData correspond to the columns
>>   of the corresponding assayData matrix.
>> 
>> Andreas Buness from arrayMagic has a use case where such a class could
>> be used to represent raw two-color microarray data.

So the use case is that one wants to subset all phenoData and
assayData components simultaneously?

I want to understand what features are desired beyond those provided
by a list of ExpressionSet instances (at first glance, a list seems
quite close to what you are asking for).

+ seth